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Package Usage : cran : treeio

Explore the latest package usage data for treeio in the cran ecosystem, including detailed information on package dependencies and their usage.

Total dependents: 107
Total downloads: 29,373
Showing first 100 dependents

More details on packages.ecosyste.ms - JSON

robertplayer/scidap-qiime2 stable

  • version: 1.22.0
Latest release: over 2 years ago - 34 downloads - 527 dependencies
btrspg/r-env cache

  • version: 1.26.0
Latest release: 10 months ago - 342 downloads - 2,231 dependencies
veitveit/coexpresso 0d86fb51b4b4cdc9a21ad900ae0f30e1eb9e828f

  • version: 1.18.1
Latest release: 5 months ago - 449 downloads - 1,733 dependencies
austinhpatton123/cogeqc-1.2.0_r-4.2.2 latest

  • version: 1.22.0
Latest release: about 3 years ago - 186 downloads - 451 dependencies
btrspg/genekitr 0.0.1

  • version: 1.25.2.001
Latest release: over 1 year ago - 204 downloads - 1,987 dependencies
weizhoujp/rchtc 4.3.0

  • version: 1.24.3
Latest release: over 2 years ago - 141 downloads - 738 dependencies
pvstodghill/pipeline-pirate 2023-11-20

  • version: 1.22.0
Latest release: about 2 years ago - 30 downloads - 347 dependencies
tariship/dev_sync_directories latest

  • version: 1.22.0
Latest release: over 2 years ago - 396 downloads - 421 dependencies
hdsu/etbii2023 latest

  • version: 1.18.1
Latest release: about 3 years ago - 138 downloads - 358 dependencies
scgfacility/rstudio-course22 v0.11

image used to run the course 2022

  • version: 1.22.0
Latest release: about 3 years ago - 195 downloads - 382 dependencies
nciccbr/ccbr_r_4.3.0 v1

  • version: 1.24.1
Latest release: over 2 years ago - 155 downloads - 679 dependencies
sviatsidorov/granie_analysis 0.1

Analysis of gliogenesis in a mouse model using GRaNIE

  • version: 1.22.0
Latest release: almost 3 years ago - 98 downloads - 290 dependencies
mattjmeier/r-odaf-hc-prod latest

  • version: 1.22.0
Latest release: about 3 years ago - 51 downloads - 897 dependencies
brianyee/cropseq-essentials 1.0.0

  • version: 1.18.0
Latest release: almost 3 years ago - 60 downloads - 2,274 dependencies
omicschef/rnaseqchef v1.1.6

RNAseqChef, an RNA-seq data controller highlighting gene expression features

  • version: 1.24.3
Latest release: 2 months ago - 1,916 downloads - 1,420 dependencies
mfsentma/atacseq latest

  • version: 1.18.1
Latest release: almost 3 years ago - 34 downloads - 852 dependencies
bac3/microbiome latest

16S rRNA gene meta-barcoding NGS data analysis app - microbioma batterico. App streamlit.

  • version: 1.22.0
Latest release: almost 3 years ago - 201 downloads - 752 dependencies
cgwyx/easymicrobiomer latest

The best practice for microbiome analysis using R

  • version: 1.25.0
Latest release: over 2 years ago - 47 downloads - 1,604 dependencies
cjchen/gxuclass 1.0

  • version: 1.24.1
Latest release: over 2 years ago - 19 downloads - 657 dependencies
avi156/rocker-binder-upd 4.2.2

  • version: 1.22.0
Latest release: almost 3 years ago - 22 downloads - 2,271 dependencies
mziemann/enrichment_recipe latest

Example highly reproducible bioinformatics workflow including transcriptome and pathway analysis.

  • version: 1.22.0
Latest release: almost 3 years ago - 62 downloads - 1,332 dependencies
albertea/numbat_light 02

  • version: 1.22.0
Latest release: over 2 years ago - 254 downloads - 301 dependencies
mattjmeier/r-odaf-hc latest

Under Development. Containerized version of the R-ODAF Health Canada Pipeline.

  • version: 1.22.0
Latest release: about 3 years ago - 33 downloads - 598 dependencies
andrewatmp/qiime_unzip latest

  • version: 1.22.0
Latest release: over 2 years ago - 151 downloads - 598 dependencies
biocorecrg/microbiomeprofile 0.4

  • version: 1.23.0
Latest release: about 2 years ago - 106 downloads - 267 dependencies
etycksen/sc_deluxe 0.7

Docker for Seurat5 and related scRNA-seq packages as well as ScanPy, SquidPy, and scvi-tools.

  • version: 1.22.0
Latest release: 9 months ago - 2,648 downloads - 757 dependencies
sornnujah/sk-bactopia-nullarbor-report alpha1

  • version: 1.18.1
Latest release: almost 3 years ago - 180 downloads - 684 dependencies
gyusikhwang/tgs v1

  • version: 1.18.1
Latest release: almost 3 years ago - 58 downloads - 1,095 dependencies
emersonchao/dsc180b latest

  • version: 1.22.0
Latest release: almost 3 years ago - 62 downloads - 2,266 dependencies
etretiakov/workbench-session-complete jammy-2024.09.19-custom-12.9

  • version: 1.25.3
Latest release: over 1 year ago - 1,193 downloads - 6,961 dependencies
mattjmeier/r-odaf-hc-base latest

  • version: 1.22.0
Latest release: about 3 years ago - 22 downloads - 598 dependencies
stormgod/deepmaps-cpu latest

  • version: 1.22.0
Latest release: almost 3 years ago - 114 downloads - 1,710 dependencies
biomehub/encodestatsbase 0.0.6

Basic docker image used as a base for EncodeStats.

  • version: 1.24.3
Latest release: about 2 years ago - 807 downloads - 853 dependencies
omicschef/epigenomechef v1.1.5

  • version: 1.24.3
Latest release: almost 2 years ago - 414 downloads - 1,066 dependencies
nfancy/scflow 0.7.4

  • version: 1.22.0
Latest release: almost 2 years ago - 300 downloads - 778 dependencies
jlphillips/csci 2025-08-08-p2

MTSU Department of Computer Science Stack

  • version: 1.22.0
Latest release: 4 months ago - 1,863 downloads - 3,823 dependencies
payne6861/clutserprofiler v1.0.0

  • version: 1.23.0
Latest release: about 3 years ago - 15 downloads - 1,793 dependencies
sheddn/bioinformatics-tools latest

  • version: 1.18.1
Latest release: about 3 years ago - 60 downloads - 2,518 dependencies
compbiocore/dscov_sct 20221201

  • version: 1.22.0
Latest release: about 3 years ago - 44 downloads - 1,031 dependencies
sebimer/samba-v4-qiime2 2024.2

  • version: 1.22.0
Latest release: almost 2 years ago - 284 downloads - 583 dependencies
compbiocore/lee_isg_erv 20230306

  • version: 1.22.0
Latest release: almost 3 years ago - 15 downloads - 1,038 dependencies
bioedge/edge_24_1_ubuntu18 20231115

  • version: 1.22.0
Latest release: about 2 years ago - 155 downloads - 2,569 dependencies
jenfisher7/rstudio_sbae latest

  • version: 1.22.0
Latest release: about 3 years ago - 40 downloads - 1,604 dependencies
bakeronit/rstudio_hpc_cancer 0.1.3

rocker-rstudio with some R packages installed in cancer genomic analysis

  • version: 1.24.3
Latest release: about 2 years ago - 110 downloads - 1,150 dependencies
jingxin/terrascpipe v0

  • version: 1.23.1
Latest release: about 3 years ago - 141 downloads - 2,467 dependencies
koki/sctensor-workshop sha-fa8c4cf

  • version: 1.17.2
Latest release: over 4 years ago - 200 downloads - 2,087 dependencies
qdidiscoveryservices/diffbind latest

  • version: 1.24.1
Latest release: over 2 years ago - 54 downloads - 526 dependencies
danhumassmed/debrowser 1.0.1

Software for Bioinformatics pipelines DEBrowser

  • version: 1.22.0
Latest release: over 2 years ago - 67 downloads - 1,319 dependencies
jackiezhuqi/bio-rstudio latest

  • version: 1.22.0
Latest release: over 2 years ago - 86 downloads - 1,158 dependencies
dcarrillouu/plot_genomes 0.2

  • version: 1.23.0
Latest release: almost 3 years ago - 82 downloads - 758 dependencies
cgrlab/qiime2 2023.5

  • version: 1.22.0
Latest release: over 2 years ago - 90 downloads - 526 dependencies
shl198/rna_ppl latest

  • version: 1.20.0
Latest release: almost 3 years ago - 24 downloads - 2,099 dependencies
gmillot/r_v4.1.2_ig_clustering_v1.1 gitlab_v9.7

https://gitlab.pasteur.fr/gmillot/dockerfiles/-/tree/v9.7

  • version: 1.18.1
Latest release: almost 3 years ago - 33 downloads - 927 dependencies
btrspg/vscode-dkd-env latest

  • version: 1.25.0.001
Latest release: almost 3 years ago - 67 downloads - 1,182 dependencies
payne6861/stereonote_non_conda_clusterprofiler_enrichplot v1.0.1

stereonote_non_conda_clusterprofiler_enrichplot

  • version: 1.23.0
Latest release: about 3 years ago - 24 downloads - 1,689 dependencies
imegusu/rstudio_rnaseq_all3 latest

RStudio based on bioconductor/bioconductor_docker:RELEASE_3_16 for RNA-Seq

  • version: 1.22.0
Latest release: over 2 years ago - 34 downloads - 1,568 dependencies
mfsentma/rna latest

  • version: 1.18.1
Latest release: almost 3 years ago - 12 downloads - 807 dependencies
firriver/crvs latest

  • version: 1.23.1
Latest release: almost 3 years ago - 53 downloads - 1,490 dependencies
ycli1995/bioinfo_dev 1.1.0

  • version: 1.24.3
Latest release: over 1 year ago - 188 downloads - 4,337 dependencies
mercury/nf_qc_scrna v2

  • version: 1.14.4
Latest release: over 2 years ago - 63 downloads - 548 dependencies
gmillot/r_v4.1.2_ig_clustering_v1.2 gitlab_v9.8

https://gitlab.pasteur.fr/gmillot/dockerfiles/-/tree/v9.8

  • version: 1.18.1
Latest release: almost 3 years ago - 19 downloads - 928 dependencies
wyangwu/r4.1.2 latest

  • version: 1.27.0
Latest release: over 2 years ago - 93 downloads - 827 dependencies
omicsclass/pan-genome v1.0

  • version: 1.22.0
Latest release: over 2 years ago - 237 downloads - 3,108 dependencies
weishwu/diffbind 3.6.5

  • version: 1.20.2
Latest release: almost 3 years ago - 31 downloads - 1,507 dependencies
viascientific/deseq2-docker 2.0

  • version: 1.22.0
Latest release: almost 3 years ago - 134 downloads - 375 dependencies
compbiocore/jupyterhub-docker-images-jh_image 20230524

  • version: 1.22.0
Latest release: over 2 years ago - 139 downloads - 3,115 dependencies
bioxfu/xseurat2 latest

  • version: 1.22.0
Latest release: almost 3 years ago - 79 downloads - 982 dependencies
wlc27/dcanr v1

  • version: 1.22.0
Latest release: almost 3 years ago - 94 downloads - 1,681 dependencies
tjhackmann/fermentationexplorer latest

  • version: 1.25.1
Latest release: about 3 years ago - 126 downloads - 827 dependencies
preethiilumina/diffbind 1.5.1

fixed genome name

  • version: 1.22.0
Latest release: about 1 year ago - 332 downloads - 626 dependencies
louisk92/spapros_scpnmf v1.0

  • version: 1.24.1
Latest release: over 2 years ago - 62 downloads - 1,422 dependencies
bianca7/mompreprocess latest

  • version: 1.25.1
Latest release: over 2 years ago - 415 downloads - 1,340 dependencies
andyvs/testimage 3.0

  • version: 1.22.0
Latest release: almost 3 years ago - 47 downloads - 376 dependencies
cbgr/cager261 1.4

Container for the CAGEr tool version 2.6.1.

  • version: 1.24.2
Latest release: almost 2 years ago - 77 downloads - 1,356 dependencies
weizhoujp/r-chtc-v1 latest

  • version: 1.24.0
Latest release: over 2 years ago - 5 downloads - 724 dependencies
bianca7/clusterprofiler latest

  • version: 1.25.4
Latest release: over 2 years ago - 62 downloads - 1,315 dependencies
fgualdr/env_gsea latest

  • version: 1.22.0
Latest release: over 2 years ago - 63 downloads - 566 dependencies
mirekphd/ml-cpu-r40-rs-cust 20230912

  • version: 1.24.2
Latest release: over 2 years ago - 29,205 downloads - 10,962 dependencies
denglab/vpfkit_base latest

  • version: 1.23.0
Latest release: almost 3 years ago - 26 downloads - 1,089 dependencies
tamaraperteghella/r4_hormonit latest

  • version: 1.18.1
Latest release: over 2 years ago - 27 downloads - 1,528 dependencies
gmillot/immcantation_v1.1 gitlab_v10.0

https://gitlab.pasteur.fr/gmillot/dockerfiles/-/tree/v10.0

  • version: 1.14.4
Latest release: almost 3 years ago - 26 downloads - 1,438 dependencies
viascientific/rstudio-app 1.0

  • version: 1.22.0
Latest release: almost 3 years ago - 127 downloads - 1,074 dependencies
anusuiya/new latest

  • version: 1.22.0
Latest release: over 2 years ago - 17 downloads - 1,329 dependencies
nfcore/airrflowreport dev

  • version: 1.22.0
Latest release: almost 3 years ago - 1,040 downloads - 409 dependencies
testalabgh/downstream signac-1.4.0

  • version: 1.18.1
Latest release: almost 3 years ago - 485 downloads - 3,517 dependencies
mbwali/jupyterlab qiime2023

  • version: 1.22.0
Latest release: over 2 years ago - 176 downloads - 1,941 dependencies
crukmi/mesa_dependencies latest

  • version: 1.22.0
Latest release: almost 3 years ago - 84 downloads - 1,393 dependencies
cmccornack/crmsc latest

  • version: 1.18.1
Latest release: over 2 years ago - 407 downloads - 1,476 dependencies
ericsalomaki/rnaseq_r4_2 latest

  • version: 1.22.0
Latest release: about 3 years ago - 69 downloads - 989 dependencies
crukmi/mesa main

  • version: 1.21.2
Latest release: over 3 years ago - 189 downloads - 1,326 dependencies
mesti90/ecoli_hgt_all_in 1.1

  • version: 1.22.0
Latest release: over 2 years ago - 282 downloads - 1,148 dependencies
omicsclass/metagenomics latest

  • version: 1.22.0
Latest release: about 2 years ago - 75 downloads - 1,493 dependencies
sridnona/r4.2.0 v1

  • version: 1.22.0
Latest release: almost 3 years ago - 98 downloads - 832 dependencies
kisudsoe/r-base latest

  • version: 1.22.0
Latest release: almost 3 years ago - 127 downloads - 1,107 dependencies
lroser/databricksbio latest

  • version: 1.24.3
Latest release: over 2 years ago - 95 downloads - 975 dependencies
ethill/qiime2 latest

docker container for qiime2

  • version: 1.22.0
Latest release: about 3 years ago - 20 downloads - 1,935 dependencies
weishwu/chipseeker 1.42.0

  • version: 1.22.0
Latest release: 4 months ago - 72 downloads - 423 dependencies
chunjiesamliu/scmocha latest

  • version: 1.24.3
Latest release: over 2 years ago - 74 downloads - 1,258 dependencies